Single-Cell RNA Sequencing of Lymph Node Stromal Cells Reveals Niche-Associated Heterogeneity

Stromal cells (SCs) establish the compartmentalization of lymphoid tissues critical to the immune response. However, the full diversity of lymph node (LN) SCs remains undefined. Using droplet-based single-cell RNA sequencing, we identified nine peripheral LN non-endothelial SC clusters. Included are the established subsets, Ccl19^hi T-zone reticular cells (TRCs), marginal reticular cells, follicular dendritic cells (FDCs), and perivascular cells. We also identified Ccl19^lo TRCs, likely including cholesterol-25-hydroxylase⁺ cells located at the T-zone perimeter, Cxcl9⁺ TRCs in the T-zone and interfollicular region, CD34⁺ SCs in the capsule and medullary vessel adventitia, indolethylamine N-methyltransferase⁺ SCs in the medullary cords, and Nr4a1⁺ SCs in several niches. These data help define how transcriptionally distinct LN SCs support niche-restricted immune functions and provide evidence that many SCs are in an activated state.